Biology subjects

Cheng, D.

Publications and source records attributed to Cheng, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The effect of prolonged elbow pain and rTMS on cortical inhibition: A TMS-EEG study

IntroductionRecent studies using combined transcranial magnetic stimulation (TMS) and electroencephalography (EEG) have shown that pain leads to an increase in the N45 peak of the TMS-evoked potential (TEP), which is mediated by GABAergic inhibition. Conversely, 10Hz repetitive TMS (10Hz-rTMS), which provides pain relief, reduces the N45 peak. However, these studies used brief pain stimuli (lasting minutes), limiting their clinical relevance. The present study determined the effect of pain and 10Hz-rTMS on the N45 peak in a prolonged pain model (lasting several days) induced by nerve growth factor (NGF) injection to the elbow muscle. Materials and MethodsExperiment 1: TEPs were measured in 22 healthy participants on Day 0 (pre-NGF), Day 2 (peak pain), and Day 7 (pain resolution). Experiment 2: We examined the effect of 5 days of active (n=16) or sham (n=16) rTMS to the left primary motor cortex (M1) on the N45 peak during prolonged NGF-induced pain, with TEPs measured on Day 0 and Day 4 (post-rTMS). ResultsExperiment 1: While no overall change in the N45 peak was seen, a correlation emerged between higher pain severity on Day 2 and a larger increase in the N45 peak. Experiment 2: Active rTMS reduced the N45 peak on Day 4 vs. Day 0, with no effect in the sham group. ConclusionOur findings suggest that (i) higher pain severity correlates with an increase in the N45 peak, and (ii) rTMS decreases cortical inhibition in a model of prolonged experimental pain. This study extends previous research by demonstrating a link between pain perception and cortical inhibition within a prolonged pain context.

neuroscience↗

bioRxiv2024

Accessible chromatin regions and DNA methylation regulate gene expression leading to changes in agronomic traits in Brassica allotriploid hybrids

IntroductionInterspecific hybridization is a common method in plant breeding to combine traits from different species, resulting in allopolyploidization and significant genetic and epigenetic changes. However, our understanding of genome-wide chromatin and gene expression dynamics during allopolyploidization remains limited. ObjectivesWe aimed to explore the relationship and underlying mechanisms between accessible chromatin regions and DNA methylation and gene transcription in genome-wide reorganization after interspecific hybridization. MethodsThis study generated two Brassica allotriploid hybrids via interspecific hybridization, combining transcriptomics, whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq), revealing that accessible chromatin regions (ACRs) and DNA methylation regulate gene expression after interspecific hybridization, ultimately influencing the agronomic traits of the hybrids. ResultsA total of 234,649 ACRs were identified in the parental lines and hybrids, the hybridization process induces changes in the distribution and abundance of there accessible chromatin regions, particularly in gene regions and their proximity. On average, genes associated with Proximal ACRs were more highly expressed than the genes associated with Distal and Genic ACRs. More than half of novel ACRs drove transgressive gene expression in the hybrids, and the transgressive up-regulated genes showed significant enrichment in metal ion binding, especially magnesium ion, calcium ion, and potassium ion binding. We also identified the Bna.bZIP11 in the single-parent activation ACR (SPA-ACR), which binds to BnaA06.UF3GT to promote anthocyanin accumulation in F1 hybrids. Additionally, in F1 hybrids, the level of DNA methylation in ACRs was higher compared to gene bodies, and the A-subgenome ACRs were associated with genome dosage rather than DNA methylation. ConclusionsThe interplay among DNA methylation, TEs, and sRNA contributes to the dynamic landscape of ACRs during interspecific hybridization, resulting in distinct gene expression patterns on the genome. HIGHLIGHTSO_LIThe study utilized the accessible chromatin regions (ACR) and DNA methylation to elucidate the mechanism behind gene expression changes following interspecific hybridization. C_LIO_LIWhole-genome recombination after interspecific hybridization leads to the rearrangement of ACR, and novel ACR and single-parent activation ACR regulate the expression of genes. C_LIO_LIDNA methylation plays a role in repressing gene expression within ACRs, and unmethylated ACRs have more transcriptionally active. C_LIO_LIA-subgenome ACRs were associated with genome dosage rather than DNA methylation. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/613586v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1504e51org.highwire.dtl.DTLVardef@145b0b8org.highwire.dtl.DTLVardef@551847org.highwire.dtl.DTLVardef@ace197_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

PGC-1α drives small cell neuroendocrine cancer progression towards an ASCL1-expressing subtype with increased mitochondrial capacity

Adenocarcinomas from multiple tissues can evolve into lethal, treatment-resistant small cell neuroendocrine (SCN) cancers comprising multiple subtypes with poorly defined metabolic characteristics. The role of metabolism in directly driving subtype determination remains unclear. Through bioinformatics analyses of thousands of patient tumors, we identified enhanced PGC-1--a potent regulator of oxidative phosphorylation (OXPHOS)--in various SCN cancers (SCNCs), closely linked with neuroendocrine differentiation. In a patient-derived prostate tissue SCNC transformation system, the ASCL1-expressing neuroendocrine subtype showed elevated PGC-1 expression and increased OXPHOS activity. Inhibition of PGC-1 and OXPHOS reduced the proliferation of SCN lung and prostate cancer cell lines and blocked SCN prostate tumor formation. Conversely, enhancing PGC- 1 and OXPHOS, validated by small-animal Positron Emission Tomography mitochondrial imaging, tripled the SCN prostate tumor formation rate and promoted commitment to the ASCL1 lineage. These results establish PGC-1 as a driver of SCNC progression and subtype determination, highlighting novel metabolic vulnerabilities in SCNCs across different tissues. STATEMENT OF SIGNIFICANCEOur study provides functional evidence that metabolic reprogramming can directly impact cancer phenotypes and establishes PGC-1-induced mitochondrial metabolism as a driver of SCNC progression and lineage determination. These mechanistic insights reveal common metabolic vulnerabilities across SCNCs originating from multiple tissues, opening new avenues for pan-SCN cancer therapeutic strategies.

cancer biology↗

bioRxiv2024

HOIL1 mediates MDA5 activation through ubiquitination of LGP2

The RIG-I-like receptors (RLRs), RIG-I and MDA5, are innate sensors of RNA virus infections that are critical for mounting a robust antiviral immune response. We have shown previously that HOIL1, a component of the Linear Ubiquitin Chain Assembly Complex (LUBAC), is essential for interferon (IFN) induction in response to viruses sensed by MDA5, but not for viruses sensed by RIG-I. LUBAC contains two unusual E3 ubiquitin ligases, HOIL1 and HOIP. HOIP generates methionine-1-linked polyubiquitin chains, whereas HOIL1 has recently been shown to conjugate ubiquitin onto serine and threonine residues. Here, we examined the differential requirement for HOIL1 and HOIP E3 ligase activities in RLR-mediated IFN induction. We determined that HOIL1 E3 ligase activity was critical for MDA5-dependent IFN induction, while HOIP E3 ligase activity played only a modest role in promoting IFN induction. HOIL1 E3 ligase promoted MDA5 oligomerization, its translocation to mitochondrial-associated membranes, and the formation of MAVS aggregates. We identified that HOIL1 can interact with and facilitate the ubiquitination of LGP2, a positive regulator of MDA5 oligomerization. In summary, our work identifies LGP2 ubiquitination by HOIL1 in facilitating the activation of MDA5 and the induction of a robust IFN response.

immunology↗

bioRxiv2024

Mutation of GmDMP genes triggers haploid induction in soybean

The development of homozygous lines is a key step in plant breeding and production. Generally, homozygous lines can be obtained through traditional time-consuming way of several generations selfing or through a way of doubled haploid (DH) technology, which has obvious advantages to accelerate breeding. However, no effective haploid production system so far has been established in soybean. Here we show that mutations of the soybean GmDMP1 and GmDMP2 genes can be used to induce haploid with an average haploid induction rate of 0.61%. We also found that 22.9% of soybean haploids can produce seeds through spontaneous chromosome doubling. Those findings laid a solid foundation for establishing DH technology in soybean, which will accelerate soybean breeding.

genetics↗

bioRxiv2024

Labeling Natural Killer cells with superparamagnetic iron oxide nanoparticles for detection by preclinical and clinical-scale magnetic particle imaging

IntroductionClinical adoption of NK cell immunotherapy is underway for medulloblastoma and osteosarcoma, however there is currently little feedback on cell fate after administration. We propose magnetic particle imaging (MPI) for the detection, localization, and quantification of VivoTrax-labeled NK cells. MethodsHuman-derived NK-92 cells were labeled by co-incubation with VivoTrax for 24 hours then the excess nanoparticles were washed with centrifugation. Cytolytic activity of labeled vs. unlabeled NK-92 cells was assessed after 4 hours of co- incubation with medulloblastoma cells (DAOY) or osteosarcoma cells (LM7 or OS17) using bioluminescent or GFP counts. Labeled NK-92 cells at two different doses (0.5 or 1 x 106) were administered to excised mouse brains (cerebellum), tibias, and lungs then imaged by 3D preclinical MPI (MOMENTUM imager) and localized relative to fiducial markers. NK-92 cells were imaged by clinical-scale MPI under development at Magnetic Insight Inc. ResultsNK-92 cells were labeled with an average of 3.17 pg Fe/cell with no measured effects on cell viability or cytolytic activity against 3 tumor cell lines. MPI signal was directly quantitative with the number of VivoTrax-labeled NK-92 cells, with preclinical limit of detection of 3.1 x 104 cells on MOMENTUM imager. Labeled NK-92 cells could be accurately localized in mouse brains, tibias, and lungs within < 1 mm of stereotactic injection coordinates with preclinical scanner. Feasibility for detection of a clinically relevant dose of 4 x 107 labeled NK-92 cells was demonstrated on clinical-scale MPI. ConclusionMPI can provide sensitive, quantitative, and accurate spatial information on NK cell delivery, showing its potential to resolve a significant unmet clinical need to track NK cell treatments in patients.

biophysics↗

bioRxiv2023

Micro-DeMix: A mixture beta-multinomial model for investigating the fecal microbiome compositions

Extensive research has uncovered the involvement of the human gut microbiome in various facets of human health, including metabolism, nutrition, physiology, and immune function. Researchers often study fecal microbiota as a proxy for understanding the gut microbiome. However, it has been demonstrated that this approach may not suffice to yield a comprehensive understanding of the entire gut microbial community. Emerging research is revealing the heterogeneity of the gut microbiome across different gastrointestinal (GI) locations in both composition and functions. While spatial metagenomics approach has been developed to address these variations in mice, limitations arise when applying it to human-subject research, primarily due to its invasive nature. With these restrictions, we introduce Micro-DeMix, a mixture beta-multinomial model that decomposes the fecal microbiome at compositional level to understand the heterogeneity of the gut microbiome across various GI locations and extract meaningful insights about the biodiversity of the gut microbiome. Moreover, Micro-DeMix facilitates the discovery of differentially abundant microbes between GI regions through a hypothesis testing framework. We utilize the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project to demonstrate the effectiveness and efficiency of the proposed Micro-DeMix. Key MessagesKey MessagesO_LIMicro-DeMix is a computational tool for understanding the heterogeneity of the gut microbiome across GI locations. C_LIO_LIMicro-DeMix facilitates the detection of differentially abundant microbes along the GI tract. C_LIO_LIMicro-DeMix detects that in IBD populations, the lower GI tract exhibits a larger abun-dance of Firmicutes and Bacteroidetes, whereas the upper GI tract is predominated by Proteobacteria and Firmicutes. C_LI

bioinformatics↗

bioRxiv2023

Polymer-based films facilitate single-step targeted expression of genetically-encoded activity sensors for in vivo microendoscopic calcium imaging

Optical methods for studying the brain offer powerful approaches for understanding how neural activity underlies complex behavior. These methods typically rely on genetically encoded sensors and actuators to monitor and control neural activity. For microendoscopic calcium imaging, injection of a virus followed by implantation of a lens probe is required to express a calcium sensor and enable optical access to the target brain region. This two-step process poses several challenges, chief among them being the risks associated with mistargeting and/or misalignment between virus expression zone, lens probe and target brain region. Here, we engineer an adeno-associated virus (AAV)-eluting polymer coating for gradient refractive index (GRIN) lenses enabling expression of a genetically encoded calcium indicator (GCaMP) directly within the brain region of interest upon implantation of the lens. This approach requires only one surgical step and guarantees alignment between GCaMP expression and lens in the brain. Additionally, the slow virus release from these coatings increases the working time for surgical implantation, expanding the brain regions and species amenable to this approach. These enhanced capabilities should accelerate neuroscience research utilizing optical methods and advance our understanding of the neural circuit mechanisms underlying brain function and behavior in health and disease.

bioengineering↗

bioRxiv2023

A novel bacterial signal transduction system specifically senses and responds to peptidoglycan damage

The peptidoglycan (PG) layer is a mesh-like structure within the cell envelope essential for maintenance of cell shape and resistance to osmotic stress, and therefore is a primary target of many important and widely used antibiotics, such as {beta}-lactams. In Gram-negative bacteria, while signal transduction systems that monitor the state of the inner- and outer-membranes have been extensively studied and well understood, much less is known about how cells sense and respond to PG-targeting stresses. Here we show that a novel bacterial two-component system (PghKR) from Shewanella oneidensis is capable of sensing and responding to PG damage. This system is specifically activated in cells exposed to various PG-targeting antibiotics or carrying a defect in PG synthesis, resulting in induced expression of blaA and relV, which encode a {beta}-lactamase conferring resistance to {beta}-lactams and a small ppGpp synthetase responsible for antibiotic tolerance, respectively. Intriguingly, the PghKR homologs are widespread among several classes of Proteobacteria and the periplasmic domain of sensor kinase PghK contains a family 9 carbohydrate-binding module that is required for signal perception, implying that the signals could be the glycan fragments of PG. Overall, our results provide critical insights into the regulation of PG homeostasis in Gram-negative bacteria.

microbiology↗

bioRxiv2023

A toxic ankyrin cysteine protease effector RipBH of brown rot triggered autophagy-associated cell death

Potato brown rot, caused by Ralstonia solanacearum, is one of the most destructive diseases of potatoes. The pathogen could hide in the tuber, leading to the rotting tubers. However, few mechanisms of pathogenesis in tubers caused by brown rot were reported. Here, we identified a highly virulent type III effector RipBH, which is not only required for the pathogenesis of potato brown rot but also displays strong cell toxicity in yeast and tobacco. We found RipBH is a novel structural cysteine protease with a large ankyrin repeat domain that contains 10 ankyrin repeats, we named it as an ankyrin cysteine protease. Biochemical analysis showed that all the ankyrin repeats are required for virulence, and the first five ankyrin repeats are indispensable for auto-cleavage site recognition. Further analysis showed that RipBH triggered autophagy-associated cell death. The ankyrin cysteine protease effector existed extensively in plant and animal pathogens suggesting the ankyrin cysteine protease effectors are functionally essential for pathogen pathogenesis. Our study enhances our understanding of this type of cysteine protease and illustrates the pathogenesis of cysteine protease in potato brown rot.

microbiology↗

bioRxiv2023

Broadly effective ACE2 decoy proteins protect mice from lethal SARS-CoV-2 infection

As SARS-CoV-2 variants have been causing increasingly serious drug resistance problem, development of broadly effective and hard-to-escape anti-SARS-CoV-2 agents is in urgent need. Here we describe further development and characterization of two SARS-CoV-2 receptor decoy proteins, ACE2-Ig-95 and ACE2-Ig-105/106. We found that both proteins had potent and robust in vitro neutralization activities against diverse SARS-CoV-2 variants including Omicron, with an average IC50 of up to 37 pM. In a stringent lethal SARS-CoV-2 infection mouse model, both proteins lowered lung viral load by up to [~]1000 fold, prevented the emergence of clinical signs in >75% animals, and increased animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously-described ACE2-Ig constructs, we found that two of these constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the RBD-binding interface should be avoided or performed with extra caution. Further, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to gram/liter level, demonstrating the developability of them as biologic drug candidates. Stress-condition stability test of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. Abstract ImportanceEngineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This study here describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously-described ACE2 decoy constructs were performed here. Two previously-described constructs with relatively more ACE2-surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Further, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broadly anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoy as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. TweetTwo antibody-like ACE2 decoy proteins could block diverse SARS-CoV-2 variants and prevent animals from severe COVID-19.

microbiology↗

bioRxiv2023

Defining T cell receptor repertoires using nanovial-based affinity and functional screening

The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired {beta}-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques. One-sentence SummaryAffinity and secretion-based screening of antigen-specific T cells using nanovials defines a functional TCR repertoire

bioengineering↗

bioRxiv2023

Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity

Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related (type 17) cells and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing ROR{gamma}t. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The CCR6+ cells phenotypes and epigenomes are stable across cell divisions under homeostatic conditions. Nonetheless, activation in polarizing and non-polarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the continuum to yield the unusual plasticity ascribed to type 17 cells.

immunology↗

bioRxiv2022

The RNA binding proteins hnRNP H and F regulate splicing of a MYC dependent HRAS exon in Prostate Cancer Cells

The Myc proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by Myc transcriptionally upregulates the core pre-mRNA splicing machinery and causes mis-regulation of alternative splicing. However, our understanding of how splicing changes are directed by Myc is limited. We performed a signaling pathway-guided splicing analysis to identify Myc dependent splicing events. These included an HRAS cassette exon repressed by Myc across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of hnRNP H gene expression with Myc hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, hnRNP F expression showed a positive correlation with Myc hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal new mechanisms for Myc-dependent regulation of splicing, and point to new possible therapeutic targets in prostate cancers. SIGNIFICANCE STATMENTMyc Transformation by the proto-oncogene c-Myc causes dysregulation of the pre-mRNA splicing reaction in cancer, but it is not known how mRNA isoform changes are directed by Myc. Here, we use bioinformatics to identify a splicing event in another proto-oncogene, HRAS, that is regulated by Myc across multiple tumor types. We identify new splicing regulators, hnRNPs H and F, that control this HRAS exon by binding to enhancer elements within its downstream intron. Additional pan-cancer bioinformatic analyses show hnRNP H expression to be anti- correlated with Myc hallmarks, consistent with the reduced splicing of the HRAS exon in Myc driven cancer. These findings uncover new mechanisms by which Myc can alter splicing in cancer cells and provide new molecular targets for potential therapeutics.

molecular biology↗

bioRxiv2022

Dlg5 and Cadherins are key to peripheral glia integrity

Glial cells in the peripheral nerve wrap axons to insulate them and ensure efficient conduction of neuronal signals. In the myelin sheath, it is proposed that the autotypic tight junctions and adherens junctions form glia-glia complexes that stabilize the glia sheath in myelinating glia. Yet the role of adhesion junctions in non-myelinating glia of vertebrates or invertebrates has not been clearly established. Many components of adhering junctions contain PDZ (PSD-95, Dlg, ZO1) domains or are recruited to these junctions by PDZ binding motifs. To test for the role of PDZ domain proteins in glial sheath formation, we carried out an RNAi screen using Drosophila melanogaster to knockdown each of the 66 predicted PDZ domain proteins in the peripheral glia. We identified six PDZ genes with potential roles in glial morphology, and further investigated Discs-large 5 (Dlg5), a scaffolding protein with no previously known function in glia. Knockdown of Dlg5 disrupts subperineurial glia (SPG) morphology, including gaps in the membrane that coincide with disruption of septate junction proteins. To further our investigation of Dlg5, we focused on cadherins and found both N-Cadherin and E-Cadherin are expressed throughout peripheral glia. Knockdown of E-Cadherin phenocopied the loss of Dlg5 leading to gaps in the SPG and septate junctions while only simultaneous loss of both N-Cadherins (NCad, and CadN2) had the same effect. The loss of all three Cadherins enhanced these phenotypes as did loss of Dlg5 when paired with cadherin knockdown. This leads to a model where Dlg5 plays a role in conjunction with cadherins in glial membrane stabilization and septate junction formation in the subperineurial glia.

neuroscience↗

bioRxiv2022

Proliferative Exhausted CD8 T Cells Exacerbate Long-lasting Anti-tumor Effects in Human Papillomavirus Positive Head and Neck Squamous Cell Carcinoma

The survival prognosis of human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) is largely different, and little is known about the anti-tumor mechanism of tumor-infiltrated CD8+ exhausted T cells (Tex) in HNSCC. We performed cell level multi-omics sequencing on human HNSCC samples to decipher the multi-dimensional characteristics of Tex cells. A proliferative exhausted CD8+ T cell cluster (P-Tex) which was beneficial to survival outcomes of patients with HPV-positive HNSCC was identified. Interestingly, P-Tex cells expressed CDK4 genes as high as cancer cells, which could be simultaneously inhibited by CDK4 inhibitors and might be a potential reason for the ineffectiveness of CDK4 inhibitors in treating HPV-positive HNSCC. P-Tex cells could aggregate in the antigen presenting cell niches and activate certain signaling pathways. Together, our findings suggest a promising role for P-Tex cells in the prognosis of patients with HPV-positive HNSCC by providing modest but persistent anti-tumor effects. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/513993v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1f8810forg.highwire.dtl.DTLVardef@1e11d84org.highwire.dtl.DTLVardef@58fb6aorg.highwire.dtl.DTLVardef@1e20a13_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

Innexin-mediated adhesion between glia is required for axon ensheathment in the peripheral nervous system

Glia are essential to protecting and enabling nervous system function and a key glial function is the formation of the glial sheath around peripheral axons. Each peripheral nerve in the Drosophila larva is ensheathed by three glial layers, which structurally support and insulate the peripheral axons. How peripheral glia communicate with each other and between layers is not well established and we investigated the role of Innexins in mediating glial function in the Drosophila periphery. Of the eight Drosophila Innexins, we found two (Inx1 and Inx2) are important for peripheral glia development. In particular loss of Inx1 and Inx2 resulted in defects in the wrapping glia leading to disruption of the glia wrap. Of interest loss of Inx2 in the subperineurial glia also resulted in defects in the neighbouring wrapping glia. Inx plaques were observed between the subperineurial glia and the wrapping glia suggesting that gap junctions link these two glial cell types. We found Inx2 is key to Ca+2 pulses in the peripheral subperineurial glia but not in the wrapping glia, and we found no evidence of gap junction communication between subperineurial and wrapping glia. Rather we have clear evidence that Inx2 plays an adhesive and channel-independent role between the subperineurial and wrapping glia to ensure the integrity of the glial wrap.

neuroscience↗

bioRxiv2022

Cell-free Tumor Methylome Analysis of Small Cell Lung Cancer Patients Identifies Subgroups with Prognostic Associations

IntroductionSmall cell lung cancer (SCLC) is a highly aggressive type of cancer with a high risk of recurrence. The SCLC methylome may yield biologic insight but is understudied due to difficulty in acquiring primary patient tissue. Here, we comprehensively profile the SCLC methylome using cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq). MethodscfDNA was extracted from plasma samples collected from 74 SCLC patients prior to initiation of first-line treatment and from 20 non-cancer smoker participants. Genomic DNA (gDNA) was also extracted from paired peripheral blood leukocytes from the 74 SCLC patients and 7 accompanying circulating-tumour-cell patient-derived xenografts (CDX). cfDNA and gDNA were used as input for cfMeDIP-seq. We developed PeRIpheral blood leukocyte MEthylation (PRIME) subtraction as an algorithm to improve tumour specificity of cell-free methylome. ResultsSCLC total plasma cfDNA methylation profiles obtained using cfMeDIP-seq are representative of CDX tumour methylation. SCLC cfDNA methylation is distinct from non-cancer plasma. Using PRIME and k-means consensus clustering, we identified two SCLC methylome clusters with prognostic associations. These clusters had methylated biological pathways related to axon guidance, neuroactive ligand-receptor interaction, pluripotency of stem cells, and were differentially methylated at long noncoding RNA, LINEs, SINEs, retrotransposons, and other repeats features. ConclusionsWe have comprehensively profiled the SCLC methylome using cfMeDIP-seq in a large patient cohort and identified methylome clusters with prognostic associations. Our work demonstrates the potential of liquid biopsies in examining SCLC biology encoded in the methylome.

cancer biology↗